VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Apr 14 2008 - 05:16:19 CDT

On Mon, 14 Apr 2008, Vlad Cojocaru wrote:

VC> Hi John, vmd users,
VC>
VC> Its clear now .. vmd-1.8.7a21 for LINUX (posted by you on the BIOCORE on the
VC> 3rd of April is compiled with python 2.5)
VC>
VC> When I installed this version on my working place (Debian, 32 bits machine),
VC> and I tried gopython it tells me "invalid command name gopython".. I did add
VC> PYTHON and NUMPY to the configure.options before running configure ...

if you download and install a binary version, changing configure.options
hast _no_ effect. this only applies to compilations.

axel.

VC>
VC> Is this happening because I do not have python 2.5 installed on my system (I
VC> only have 2.4)?
VC>
VC> Best
VC> vlad
VC>
VC>
VC> Vlad Cojocaru wrote:
VC> > Hi John,
VC> >
VC> > I believe you are right .. It should not matter whether those files are
VC> > executables. I've just thought that the permissions might have changed
VC> > while I checked out the files and that's why I asked. But if they were
VC> > checked in like this and if this is more convenient from your side, it
VC> > should be fine ... There is no reason to affect the compilation itself.
VC> >
VC> > Are the latest test version (1.8.7a19) already compiled with python 2.5
VC> > and tcl 8.5? What Numeric version do you use for compiling ?
VC> >
VC> > Best wishes
VC> > vlad
VC> >
VC> >
VC> >
VC> > John Stone wrote:
VC> > > Hi guys,
VC> > > I believe the source files in public CVS may be marked as executable
VC> > > because we have scripts that copy our internal CVS repository to the
VC> > > externally
VC> > > accessible server. The scripts may do chmod -R ... type operations
VC> > > to make it impossible for CVS permissions to prevent access to the files
VC> > > by the unprivileged CVS server process. I haven't looked at the scripts
VC> > > in years, but that's my vague recollection. It shouldn't harm anything,
VC> > > though it may offend your sense of cleanliness to see all those source
VC> > > files set to be executable. :) I can look into this more closely if
VC> > > people actually care, but thus far it has never mattered to my
VC> > > knowledge,
VC> > > and it has prevented bad permissions in our internal tree from creating
VC> > > problems for external developers working from the public CVS.
VC> > >
VC> > > Cheers,
VC> > > John
VC> > >
VC> > > On Sun, Apr 13, 2008 at 04:00:12PM -0400, Axel Kohlmeyer wrote:
VC> > >
VC> > > > On Sun, 13 Apr 2008, Cojocaru,Vlad wrote:
VC> > > >
VC> > > > VC> Hi Alex,
VC> > > > VC>
VC> > > > VC> Thanks for replying !!
VC> > > > VC>
VC> > > >
VC> > > > VC> I had openSuse 10.0 and upgraded to the new 10.3 (on Athlon 64,
VC> > > > VC> 3500+)... I have just seen that all the checkout files were
VC> > > > VC> executables on my machine after checkout with cvs following
VC> > > > VC> exactly the recipe on the VMD web site ... I cannot explain why
VC> > > > VC> all files were executables if by default the permissions are
VC> > > > VC> preserved ...
VC> > > >
VC> > > > probably because they were checked in like this...
VC> > > > i checked my checkout and most, but not all files are executable.
VC> > > > it never made a difference in compiling, so...
VC> > > >
VC> > > > VC> Regarding my second question, I think you misunderstood ... I
VC> > > > VC> first downloaded the binaries for vmd-1.8.7a19 ... And with these
VC> > > > VC> binaries I had the python problem ... After seeing the problem
VC> > > > VC> (and having
VC> > > >
VC> > > > well, since you have suse and john is compiling on red hat, i'm not
VC> > > > surprised that there may be (small) differences. you'd have to install
VC> >>> _his_ compile of the python parts. if i remember correctly, he is not
VC> > > > building with tcl 8.5 (not 8.4), on top of that...
VC> > > >
VC> > > > with the diversity of distributions and the ways how people install
VC> > > > (or mutilate) them, the only way to have a binary consistent with your
VC> > > > distribution is to compile yourself. :-(
VC> > > >
VC> > > > VC> the problem so many times before with vmd versions earlier than
VC> > > > VC> 1.8.6) I thought that the simple solution is just to compile vmd
VC> > > > VC> and as I did it before I should be able to do it again ... And
VC> > > > VC> that's when I downloaded the code from CVS
VC> > > > VC>
VC> > > > VC> I did not do the compilation yet ...
VC> > > >
VC> > > > good luck,
VC> > > > axel.
VC> > > >
VC> > > >
VC> > > > VC> bets wishes
VC> > > > VC> vlad
VC> > > > VC>
VC> > > > VC>
VC> > > >
VC> > > > --
VC> > > > =======================================================================
VC> > > > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
VC> > > > http://www.cmm.upenn.edu
VC> > > > Center for Molecular Modeling -- University of Pennsylvania
VC> > > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
VC> > > > 19104-6323
VC> > > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
VC> > > > =======================================================================
VC> > > > If you make something idiot-proof, the universe creates a better
VC> > > > idiot.
VC> > > >
VC> > >
VC> > >
VC> >
VC> > --
VC> > ----------------------------------------------------------------------------
VC> > Dr. Vlad Cojocaru
VC> >
VC> > EML Research gGmbH
VC> > Schloss-Wolfsbrunnenweg 33
VC> > 69118 Heidelberg
VC> >
VC> > Tel: ++49-6221-533266
VC> > Fax: ++49-6221-533298
VC> >
VC> > e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
VC> >
VC> > http://projects.villa-bosch.de/mcm/people/cojocaru/
VC> >
VC> > ----------------------------------------------------------------------------
VC> > EML Research gGmbH
VC> > Amtgericht Mannheim / HRB 337446
VC> > Managing Partner: Dr. h.c. Klaus Tschira
VC> > Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
VC> > http://www.eml-r.org
VC> > ----------------------------------------------------------------------------
VC> >
VC> >
VC>
VC> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.